|
| Status |
Public on Nov 21, 2013 |
| Title |
WAT_WT_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
WAT_WT
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57Bl/6J
genotype/variation: wild type
gender: male
age: 17 weeks
tissue: epididymal adipose tissue
|
| Treatment protocol |
Male wild type C57BL/6 mice and aP2-XBP1 transgenic mice were grown until the age of 17 weeks while being fed chow (Harlan Teklad #2914). Animals were then killed and epididymal white adipose tissue was removed. Total RNA was isolated and subjected to gene expression profiling.
|
| Growth protocol |
Transgenic mice overespressing XBP1 in adipose tissue were were generated on a C57Bl/6J background. Age-matched wild-type C57Bl/6J mice were used as control mice. Mice were housed under standard conditions with a 12-hour light-dark cycle and were fed a standard mouse chow diet with free access to water. Experiments were performed in 17-week old animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from adipose tissue using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
|
| Label |
biotin
|
| Label protocol |
The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.
|
| |
|
| Hybridization protocol |
Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).
|
| Scan protocol |
Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
|
| Description |
epididymal adipose tissue, wild type mouse, replicate 4
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.18.1).
|
| |
|
| Submission date |
Feb 23, 2012 |
| Last update date |
Nov 22, 2013 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE36031 |
Adipocyte XBP1s regulates systemic insulin sensitivity by modulating adiponectin multimerization |
|
